Modding inside MO

I have run up against some obstacles... First, I have an installed mod that I now want to modify on-the-fly so to speak. I want to change some of its bits and pieces (nif branch pruning, replacing, texture color shifting...Stuff like that). How best to do this without messing up the original mod?

And then there is the CK. I haven't tried this yet, so A: Do I just use it (through MO of course...) and B: If I modify the original esp / esm is it just for that profile, or am I modding the base?

And, the worst of all... I am using bodyslide to create profiles for not just bodies, but also for wearables. I typically use two body types, CBBE and UNPB. The UNPB only for my principal follower, CBBE for the rest. So I usually move my CBBE meshes and textures into backup folders, then copy in my UNPB stuff, make my changes on bodies and outfits, then move all of that product to where it should go, copy-pasta back my CBBE stuff, modify it... Hmm. Let me see if I can show the folder structure that I normally use... I'll use textures, meshes is pretty much the same.

Data\textures\actors\character\female is the primary folder. Inside that I will have four other folders

Primary Follower

Primary follower backup

NPC's

NPC's Backup

So, I essentially have two sets of each type of body texture, plus the active set in the \female folder. Make the changes, test in-game, if I am satisfied, copy into the appropriate folder (primary follower or npc). When I am really sure, or perhaps later on in the game I see something that needs changing, I copy the primary follower or npc folder to its backup, clear out the \female folder, copy in the primary follower or npc folder contents, then make my changes, do some testing, then commit the changes back into the follower or npc folder. So my backup folders are always one revision behind. Is that muddy enough? (and then there are the facegendata folders....)

There are several ways to do this when using MO. One way is to use a single folder for a mod and use the "Hide" function to temporarily hide or unhide selected folders or even individual resources in a folder. Another way is to use several different folders for a mod each with a separate and potentially different version of a mod. Profiles don't help you very much directly for this since all profiles use the same set of mod folders; profiles allow you to select which mods to use but each mod folder is the same across all profiles. You might even want to use combination of the two methods.

If you use the CK you will want at least two copies of the mod, the original unedited version and one or more edited versions in different mod folders for your testing.

I would strongly advise against using the CK through MO. You may find yourself encountering several crashes and/or unwanted overwrites (plus other numerous burdens).

For other modding activities you can do as Kelmych says, although the general consensus is to always mod outside MO. At least this is what I always do and never encountered a single issue (repeat, especially with CK both in classic (not using it anymore) and in SSE)

xEdit can be an exception to this especially when used for patching purposes.

If you can spare the disk-size, I do recommend to duplicate your Skyrim installation, extract all BSAs, put in there all your modding tools and...sky is the limit!

Any issues you may face with editing plugins with the CK via MO are NOT the fault of MO. It is just a tool to provide a set of mods to either the game engine, or in this instance, the Construction Kit.

Crashes are just part and parcel of the crappy tools Bethesda supplies the user and any "unwanted" overwrites are due to the user not being aware of what files are being saved and where.